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Chromosome organization and gene expansion in the highly fragmented genome of the ciliate Strombidium stylifer

Journal of Genetics and Genomics 2021年第10期48卷 908-916页

作者： Chao Li Xiao Chen Weibo Zheng Thomas G.Doak Guangyi Fan Weibo Song Ying Yan Institute of Evolution&Marine Biodiversity Ocean University of ChinaQingdao 266003China Marine College Shandong UniversityWeihai 264209China School of Life Sciences Ludong UniversityYantai 264025China Department of Biology Indiana UniversityBloomingtonIN 47405USA National Center for Genome Analysis Support Indiana UniversityBloomingtonIN 47405USA BGI-Qingdao BGI-ShenzhenQingdao 266555China State Key Laboratory of Agricultural Genomics BGI-ShenzhenShenzhen 518083China Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and TechnologyQingdao 266237China

Chromosomes are well-organized carriers of genetic information in eukaryotes and are usually quite long,carrying hundreds and thousands of ***,a clade of single-celled ciliates,Spirotrichea,feature nanochromosomes—also called“gene-sized chromosomes”.These chromosomes predominantly carry only one gene,flanked by short telomere ***,the organization and copy number variation of the chromosomes in these highly fragmented genomes remain unexplored in many groups of Spirotrichea,including the marine *** deep genome sequencing,we assembled the macronuclear genome of Strombidium stylifer into more than 18,000 nanochromosomes(~2.4 Kb long on average).Our results show that *** occupies an intermediate position during the evolutionary history of Strombidium lineage and experienced significant expansions in several gene families related to guanyl ribonucleotide *** on the nucleotide distribution bias analysis and conserved motifs search in non-genic regions,we found that the subtelomeric regions have a conserved adenine-thymine(AT)-rich sequence *** also found that the copy number of nanochromosomes lacks precise *** work sheds light on the unique features of chromosome structure in eukaryotes with highly fragmented genomes and reveals that a rather specialized evolutionary strategy at the genomic level has resulted in great diversity within the ciliated lineages.

关键词： ciliate Copy number Nanochromosome Nucleotide distribution bias Strombidium stylifer

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Morphological and molecular examination of the ciliate family Lagynusidae(Protista,Ciliophora,Prostomatea)with descriptions of two new genera and two new species from China

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Marine Life Science & Technology 2023年第2期5卷 178-195页

作者： Limin Jiang Congcong Wang Saleh A.Al-Farraj Hunter N.Hines Xiaozhong Hu College of Fisheries and Key Laboratory of MaricultureMinistry of EducationOcean University of ChinaQingdao 266003China Institute of Evolution and Marine Biodiversity Ocean University of ChinaQingdao 266003China Department of Zoology College of ScienceKing Saud UniversityRiyadh 11451Saudi Arabia Harbor Branch Oceanographic Institute Florida Atlantic UniversityFort PierceFL 34982USA

ciliates in the class Prostomatea play an important role in the global microbial loop due to their signifcant abundances and broad feeding strategies at the foundation of food *** their importance in ecosystems,the taxonomy and systematics of this group of ciliates has long been poorly understood,with this being especially true for members of the family *** we examine four lagynusids collected from sandy beaches in China,using silver-staining and 18S rRNA gene sequencing *** investigations revealed two new genera and two new species and provided details for two little known forms:Penardella marina ***.,***.,Apolagynus cucumis(as reported by Penard.Études sur les infusoires d’eau *** and Cie,Genève,1922)***.,***.,Lagynus minutus ***.,and Lagynus elegans(Engelmann in Z Wiss Zool 11:347-393,1862)Quennerstedt(Acta Univ Lund 4:1-48,1867).Penardella *** be morphologically distinguished by having more than three dikinetidal perioral *** *** from the closely related genus Lagynus in the absence of a conspicuous neck-like *** ciliature of Apolagynus cucumis is revealed here for the frst time,which demonstrates the classifcation of this species within ***,Apolagynus binucleatus(Jiang et al.,2021)*** established according to the new *** results of our phylogenetic analyses based on the 18S rRNA gene support the establishment of two new genera and indicate that Lagynusidae is monophyletic,which further strengthens its valid taxonomic status.

关键词： ciliate Morphology New genus New species Phylogeny 18S rRNA gene

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Toxicity of Chlorpyrifos and Dimethoate to the ciliate Urostyla grandis, with Notes on Their Effects on Cell Ultrastructure

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Journal of Ocean University of China 2018年第3期17卷 697-704页

作者： MU Weijie WARREN Alan PAN Xuming YING Chen College of Life Science and Technology Harbin Normal University Department of Life Sciences Natural History MuseumLondon

Chlorpyrifos and dimethoate are overused agricultural pesticides that can trigger trophic cascades, resulting in toxicity to both terrestrial and aquatic organisms as well as altered ecosystems. In previous studies, substantial attention has been given to the effects of pesticides on vertebrate species and, to a lesser extent, species of zooplankton. The present study was designed to show that the fission time effective concentration in ciliates is a potential aquatic detection index for environmental monitoring. The ciliate Urostyla grandis was treated with doses of chlorpyrifos and dimethoate. After exposed to the pesticides, the LC_(50)(i.e., concentration that killed 50% of the ciliate cells within 24 h) values were 0.029 mg L^(-1) for chlorpyrifos and 0.0685 mg L^(-1) for dimethoate. The fission time effective concentrations after 168 h of exposure were 0.0075–0.0093 mg L^(-1) for chlorpyrifos and 0.2640–0.2750 mg L^(-1) for dimethoate. These results show that the fission time effective concentration is lower than the LC_(50) value in ciliates, indicating that fission time effective concentration is more suitable than the LC_(50) value for environmental monitoring using ciliates. The effects of chlorpyrifos and dimethoate on ciliate cell ultrastructures included agglutination of chromatin in the macronucleus, protruded and discontinuous macronuclear and micronuclear membranes, loss of integrity of mitochondrial membranes and contents, and abscission and deformation of the adoral zone of membranelles.

关键词： ciliate fission time effective concentration LC50 pesticide ultrastructure

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Taxonomy, Morphology and Phylogeny of a New Oligotrich ciliate-Omegastrombidium hongkongense n. sp.(Protozoa: Ciliophora) from Clear Water Bay, Hong Kong

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Journal of Ocean University of China 2018年第4期17卷 890-896页

作者： SHEN Zhuo LIU Weiwei ZHANG Shuwen YI Zhenzhen LIU Hongbin Microbial Ecology and Matter Cycle Group School of Marine Sciences Sun Yat-sen University Coastal Marine Laboratory The Hong Kong University of Science and Technology Key Laboratory of Tropical Marine Bio-Resources and Ecology South China Sea Institute of Oceanology Chinese Academy of Science Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring School of Life Science South China Normal University

One new marine oligotrich ciliate, Omegastrombidium hongkongense n. sp., was isolated from a bloom of Noctiluca scuntillans near Port Shelter, Hong Kong. The morphology and infraciliature of this new species were studied on both living and protargol-stained specimens. Its phylogenetic position was discussed based on the sequence of the small subunit r RNA gene. O. hongkongense is different from its congeners with special characters. The cells are usually heart-shaped, and the cell size usually is(20–35) ×(20–30) μm in vivo. Its deep buccal cavity extends obliquely to about 1/2 of cell length. It shows prominent apical protrusion. The adoral zone of membranelles is divided into 17–19 collar membranelles and four buccal membranelles. It has one ball-like macronucleus. The girdle kinety forms a closed loop which obliquely surrounds the body. The ventral kinety and thigmotactic membranelles are not observed. The SSU r RNA sequence of O. hongkongense was close to those of Strombidium paracalkinsi and Varistrombidium kelum with approximately 99% similarity. In the phylogenetic trees, O. hongkongense can be grouped with O. elegans and V. kielum species with very low support(16% ML).

关键词： infraciliature marine ciliate morphology Oligotrichia Noctiluca scuntillans

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Salinity Acclimation Induces Reduced Energy Metabolism,Osmotic Pressure Regulation and Transcriptional Reprogramming in Hypotrichida ciliate Gastrostyla setifera

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Journal of Ocean University of China 2024年第2期23卷 539-549页

作者： JI Xin BI Luping ZOU Songbao LI Wenlu JI Daode ZHANG Qianqian School of Ocean Yantai UniversityYantai 264005China Key Laboratory of Coastal Environmental Processes and Ecological Remediation Yantai Institute of Coastal Zone ResearchChinese Academy of SciencesYantai 264003China Zhejiang Institute of Freshwater Fisheries Huzhou 313001China Muping Coastal Environment Research Station Yantai Institute of Coastal Zone ResearchChinese Academy of SciencesYantai 264117China

Coastal and estuarine protists are frequently exposed to salinity *** the tolerance and stress responses of microalgae to salinity have been extensively studied,there have been scarce studies on the physiological response of heterotrophic protists to salinity *** this study,we investigated the physiological response of the heterotrophic ciliate Gastrostyla setifera to a salinity of 3,via a transcriptomic *** first transcriptome of genus Gastrostyla was obtained utilizing a group of manually isolated ciliate individuals(cells)and RNA-seq *** completeness of the transcriptome was *** expressed gene(DEG)analysis was performed among the transcriptomes of *** acclimated in saline water(salinity 3)and those cultured in fresh *** results demonstrated a significant alternation in gene transcription,in which the ciliate exhibits a transcripttomic acclimation in responding salinity *** up-regulated DEGs were enriched in the pathways of cytoskeleton proteins,membrane trafficking,protein kinases and protein *** may represent enhanced functions of ion transport,stress response and cell *** involved in energy metabolism and biosynthesis were markedly down-regulated,reflecting decreased cell ***,we detected significantly down-regulated genes involved in several pathways of amino acid catabolism,which may lead to accumulation of amino acids in the ciliate *** acid could act as compatible solutes in the cytoplasm to maintain the osmotic balance in saline ***,this work is an initial exploration to the molecular basis of the heterotrophic protist responding to salinity *** result sheds light on the mechanisms of enhancement of cell protection,reduction of cell activity,and osmotic pressure regulation in ciliates acclimated to salinity.

关键词： salinity stress heterotrophic protist ciliate Gastrostyla setifera transcriptome differentially expressed gene

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Observations on a magnetotactic bacteria-grazing ciliate in sediment from the intertidal zone of Huiquan Bay,China

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Journal of Oceanology and Limnology 2021年第6期39卷 2053-2062页

作者： Si CHEN Kaixuan CUI Wenyan ZHANG Yicong ZHAO Tian XIAO Hongmiao PAN Wuchang ZHANG Long-Fei WU CAS Key Laboratory of Marine Ecology and Environmental Sciences Institute of OceanologyChinese Academy of SciencesQingdao 266071China University of Chinese Academy of Sciences Beijing 100049China Laboratory for Marine Ecology and Environmental Science Pilot National Laboratory for Marine Science and Technology(Qingdao)Qingdao 266237China Center for Ocean Mega-Science Chinese Academy of SciencesQingdao 266071China International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms(LIA-MagMC) CNRS-CASQingdao 266071China Aix Marseille Univ CNRSLCBIM2BIMMMarseille 13009France

Magnetotactic bacteria(MTB)are a group of prokaryotes having the ability to orient and swim along geomagnetic field lines because they contain intracellular magnetosomes that are synthesized through a biomineralization *** have recently also been found in unicellular eukaryotes,which are referred to as magnetically responsive protists(MRPs).The magnetosomes have three origins in *** this study,we characterized a MTB-grazing ciliated MRP that was magnetically collected from intertidal sediment of Huiquan Bay,Qingdao,*** on 18S rRNA gene sequence analysis,the ciliated MRP was tentatively identified as Uronemella parafi lificum *** transmission electron microscopy,we observed that magnetosomes having 2-3 shapes were randomly distributed within this *** X-ray spectroscopy and high-resolution transmission electron microscopy images of the magnetosomes were consistent with them being composed of *** having the same shape and mineral composition were also detected in MTB that occurred in the same environment as the ciliated *** analysis showed that the size and shape of the magnetosomes in the ciliated MRP were similar to those in *** results suggest that this ciliated MRP can graze,ingest,and digest various types of *** is certainly worth noting that this is the first record of MRPs in Asian aquatic sediment and suggesting they might be widely *** results also support the assertion that MRPs probably contribute to the ecological cycles of iron,and expand possibilities for research into the mechanism of magnetoreception in eukaryotes.

关键词： magnetically responsive protist ciliate magnetotactic bacteria magnetosome graze magnetoreception

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A practical reference for studying meiosis in the model ciliate Tetrahymena thermophila

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Marine Life Science & Technology 2022年第4期4卷 595-608页

作者： Miao Tian Xia Cai Yujie Liu Mingmei Liucong Rachel Howard-Till Institute of Evolution&Marine Biodiversity Ocean University of ChinaQingdao266003China Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and TechnologyQingdao266237China Department of Molecular and Cellular Biology University of California DavisDavisCAUSA Institute of Human Genetics CNRSUniversity of Montpellier34090MontpellierFrance

Meiosis is a critical cell division program that produces haploid gametes for sexual *** in meiosis are often causes of infertility and birth defects(e.g.,Down syndrome).Most organisms use a highly specialized zipper-like protein complex,the synaptonemal complex(SC),to guide and stabilize pairing of homologous chromosomes in *** the SC is critical for meiosis in many eukaryotes,there are organisms that perform meiosis without a functional ***,such SC-less meiosis is poorly *** understand the features of SC-less meiosis and its adaptive significance,the ciliated protozoan Tetrahymena was selected as a *** research in Tetrahymena has revealed intriguing aspects of the regulatory programs utilized in its SC-less meiosis,yet additional efforts are needed for obtaining an in-depth comprehension of mechanisms that are associated with the absence of ***,aiming at promoting a wider application of Tetrahymena for meiosis research,we introduce basic concepts and core techniques for studying meiosis in Tetrahymena and then suggest future directions for expanding the current Tetrahymena meiosis research *** methodologies could be adopted for dissecting meiosis in poorly characterized ciliates that might reveal novel *** data will hopefully provide insights into the function of the SC and the evolution of meiosis from a unique perspective.

关键词： Meiosis ciliate Tetrahymena Synaptonemal complex Cytogenetics

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SHORT TIME DYNAMICS OF ciliate ABUNDANCE IN THE BOHAI SEA (CHINA)

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Chinese Journal of Oceanology and Limnology 2002年第2期20卷 135-141页

作者：张武昌王荣 Marine Ecology Department Institute of Oceanology Chinese Academy of Sciences 266071 Qingdao China

The ciliate community in the Bohai Sea (China) was studied from 23 September to 7 October 1998. A hurricane struck the study area between the two grid station investigations, which were six days apart. Six tintinnid species (Favella panamensis, Leptotintinnus nordqvisti, Tintinnopsis butschlii, T. karajacensis, T. Radix and Wangiella dicollaria) were identified. Total cililate abundance in the surface layer ranged from 20 to 770 ind/l. In the first grid investigation, Tintinnopsis karajacensis dominated in the warm, low salinity waters at the Huanghe River mouth. Aloricate ciliate sp.1 dominated in the cold, high salinity waters in the northwest of the study area and the Bohai Strait. In the second grid investigation, T. Karajacensis almost disappeared. The abundance of aloricate ciliate sp.1 decreased drastically. The aloricate ciliate sp.2 dominated at the Bohai Strait. The change of ciliate abundance may be due to the disturbance of hurricane.

关键词： ciliate tintinnid microzooplankton Bohai Sea

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An improved method for tubulin staining of ciliated eukaryotes

Water Biology and Security

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Water Biology and Security 2024年第3期3卷 65-71页

作者： Tingting Pan Jing Zhang Che Hu Guanxiong Yan Weiwei Qin Zixin Cheng Dongxia Yuan Fang Zhou Jie Xiong Wei Miao Chuanqi Jiang Institute of Hydrobiology Chinese Academy of SciencesWuhanChina University of Chinese Academy of Sciences BeijingChina Harbin Normal University HarbinChina Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture Chinese Academy of SciencesWuhanChina Hubei Hongshan Laboratory WuhanChina Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation Beibu Gulf UniversityQinzhouChina

ciliated microeukaryotes(ciliates)are distinguished by their cilia,which are rich in *** developed a method for tubulin staining in ciliate cells that involves using live-cell tubulin-staining dyes instead of antibodies thereby streamlining the staining process,which is effective across diverse ciliate ***,our method allows integration with immunofluorescence staining using antibodies when *** potential applications of this technique extend to cell biology and ciliate morphological and ecological studies.

关键词： ciliate Cilium Live-cell tubulin dye Tubulin staining

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SPECIES COMPOSITION AND SEASONAL DENSITY DYNAMICS OF ciliateD PROTOZOA IN BAOAN LAKE WITH PARTICULAR REFERENCE TO THE SUBMERGED MACROPHYTES

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Chinese Journal of Oceanology and Limnology 1999年第1期17卷 86-96,79页

作者：宋碧玉谢平 Department of Environmental Engineering Wuhan University of Hydraulic and Electric Engineering Wuhan China Institute of Hydrobiology Chinese Academy of Sciences Wuhan China National Institute for Environmental Studies Tsukuba Ibaraki Japan

From April 1996 to October 1997, regular samplings were carried out monthly at 8 stations in a macrophytic basin of Baoan Lake. From the water samples, 47 genera, 96 species of ciliata were identified. Stations covered with macrophytes had greater number of ciliate species and higher percentage of sessile species. The mixotroph Strombidium viride bearing algal endosymbionts dominated numerically the whole ciliate communities; most of the other dominants were bactivores. Total ciliate density in Lake Baoan was 6170-34310 ind./L. The seasonal density fluctuations of the dominant species populations were also investigated. Maximum abundances were observed in spring and winter during the decay of macrophytes and minimum densities were observed during the summer months of luxuriant macrophytes growth.

关键词： Protozoa ciliate Baoan Lake macrophytic lake

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